Biodegradation of drotaverine hydrochloride by free and immobilized cells of Rhodococcus rhodochrous IEGM 608

Bioinformatics Analysis of the Genome of Rhodococcus rhodochrous IEGM 1362, an (-)-Isopulegol Biotransformer

A genome of Rhodococcus rhodochrous IEGM 1362 was sequenced and annotated. This strain can transform monoterpene alcohol (-)-isopulegol with the formation of two novel pharmacologically promising metabolites. Nine genes encoding cytochrome P450, presumably involved in (-)-isopulegol transformation, were found in the genome of R. rhodochrous IEGM 1362. Primers and PCR conditions for their detection were selected. The obtained data can be used for the further investigation of genes encoding enzymes involved in monoterpene biotransformation.

Selective enrichment, identification, and isolation of diclofenac, ibuprofen, and carbamazepine degrading bacteria from a groundwater biofilm

Diclofenac, ibuprofen, and carbamazepine are three of the most widely detected and most concerning pharmaceutical residues in aquatic ecosystems. The aim of this study was to identify bacteria that may be involved in their degradation from a bacterial biofilm. Selective enrichment cultures in mineral salt solution containing pharmaceutical compounds as sole source of carbon and energy were set up, and population dynamics were monitored using shotgun metagenome sequencing. Bacterial genomes were reconstructed using genome-resolved metagenomics. Thirty bacterial isolates were obtained, identified at species level, and tested regarding pharmaceutical biodegradation at an initial concentration of 1.5 mg l-1. The results indicated that most probably diclofenac biodegrading cultures consisted of members of genera Ferrovibrio, Hydrocarboniphaga, Zavarzinia, and Sphingopyxis, while in ibuprofen biodegradation Nocardioides and Starkeya, and in carbamazepine biodegradation Nocardioides, Pseudonocardia, and Sphingopyxis might be involved. During the enrichments, compared to the initial state the percentage relative abundance of these genera increased up to three orders of magnitude. Except Starkeya, the genomes of these bacteria were reconstructed and annotated. Metabolic analyses of the annotated genomes indicated that these bacteria harbored genes associated with pharmaceutical biodegradation. Stenotrophomonas humi DIC_5 and Rhizobium daejeonense IBU_18 isolates eliminated diclofenac and ibuprofen during the tests in the presence of either glucose (3 g l-1) or in R2A broth. Higher than 90% concentration reduction was observed in the case of both compounds.

Bioremediation of Oil-Contaminated Soil of the Republic of Kazakhstan Using a New Biopreparation

A new biopreparation is developed to clean soils from oil pollution in the arid climate of the Republic of Kazakhstan. The biopreparation includes bacterial strains R. qingshengii F2-1, R. qingshengii F2-2, and P. alloputida BS3701. When using the biopreparation in a liquid mineral medium with 15% crude oil, laboratory studies have revealed degradation of 48% n-alkanes and 39% of PAHs after 50 days. The effectiveness of the biopreparation has been demonstrated in field experiments in the soil contaminated with 10% crude oil at the K-Kurylys landfill, Republic of Kazakhstan. During the six-month field experiment, the number of oil degraders reached 10⁷ CFU/g soil, which degraded 70% of crude oil by the end of the experiment.

Rhodococcus strains as a good biotool for neutralizing pharmaceutical pollutants and obtaining therapeutically valuable products: Through the past into the future

Active pharmaceutical ingredients present a substantial risk when they reach the environment and drinking water sources. As a new type of dangerous pollutants with high chemical resistance and pronounced biological effects, they accumulate everywhere, often in significant concentrations (μg/L) in ecological environments, food chains, organs of farm animals and humans, and cause an intense response from the aquatic and soil microbiota. Rhodococcus spp. (Actinomycetia class), which occupy a dominant position in polluted ecosystems, stand out among other microorganisms with the greatest variety of degradable pollutants and participate in natural attenuation, are considered as active agents with high transforming and degrading impacts on pharmaceutical compounds. Many representatives of rhodococci are promising as unique sources of specific transforming enzymes, quorum quenching tools, natural products and novel antimicrobials, biosurfactants and nanostructures. The review presents the latest knowledge and current trends regarding the use of Rhodococcus spp. in the processes of pharmaceutical pollutants’ biodegradation, as well as in the fields of biocatalysis and biotechnology for the production of targeted pharmaceutical products. The current literature sources presented in the review can be helpful in future research programs aimed at promoting Rhodococcus spp. as potential biodegraders and biotransformers to control pharmaceutical pollution in the environment.

Cellular Modifications of Rhodococci Exposed to Separate and Combined Effects of Pharmaceutical Pollutants

Actinomycetes of the genus Rhodococcus (class Actinomycetia) are dominant dwellers of biotopes with anthropogenic load. They serve as a natural system of primary response to xenobiotics in open ecosystems, initiate defensive responses in the presence of pollutants, and are regarded as ideal agents capable of transforming and degrading pharmaceuticals. Here, the ability of selected Rhodococcus strains to co-metabolize nonsteroidal anti-inflammatory drugs (ibuprofen, meloxicam, and naproxen) and information on the protective mechanisms of rhodococci against toxic effects of pharmaceuticals, individually or in a mixture, have been demonstrated. For the first time, R. ruber IEGM 439 provided complete decomposition of 100 mg/L meloxicam after seven days. It was shown that versatile cellular modifications occurring at the early development stages of nonspecific reactions of Rhodococcus spp. in response to separate and combined effects of the tested pharmaceuticals included changes in electrokinetic characteristics and catalase activity; transition from unicellular to multicellular life forms accompanied by pronounced morphological abnormalities; changes in the average size of vegetative cells and surface area-to-volume ratio; and the formation of linked cell assemblages. The obtained data are considered as adaptation mechanisms in rhodococci, and consequently their increased resistance to separate and combined effects of ibuprofen, meloxicam, and naproxen.

The Use of Baikal Psychrophilic Actinobacteria for Synthesis of Biologically Active Natural Products from Sawdust Waste

One of the relevant areas in microbiology and biotechnology is the study of microorganisms that induce the destruction of different materials, buildings, and machines and lead to negative effects. At the same time, the positive ecological effects of degradation can be explained by the detoxication of industrial and agricultural wastes, chemical substances, petroleum products, xenobiotics, pesticides, and other chemical pollutants. Many of these industrial wastes include hard-to-degrade components, such as lignocellulose or plastics. The biosynthesis of natural products based on the transformation of lignocellulosic wastes is of particular interest. One of the world’s unique ecosystems is presented by Lake Baikal. This ecosystem is characterized by the highest level of biodiversity, low temperatures, and a high purity of the water. Here, we studied the ability of several psychrophilic representatives of Baikal Actinobacteria to grow on sawdust wastes and transform them into bioactive natural products. Different strains of both widely spread genus of Actinobacteria and rare genera of Actinobacteria were tested. We used the LC-MS methods to show that Actinobacteria living in sawmill wastes can produce both known and novel natural products with antibiotic activity. We demonstrated that the type of sawmill wastes and their concentration influence the Actinobacteria biosynthetic potential. We have shown for the first time that the use of Baikal psychrophilic microorganisms as a factory for biodegradation is applicable for the transformation of lignocellulosic wastes. Thus, the development of techniques for screening novel natural products leads to an elaboration on the active ingredients for novel drugs.

Response of Rhodococcus cerastii IEGM 1278 to toxic effects of ibuprofen

The article expands our knowledge on the variety of biodegraders of ibuprofen, one of the most frequently detected non-steroidal anti-inflammatory drugs in the environment. We studied the dynamics of ibuprofen decomposition and its relationship with the physiological status of bacteria and with additional carbon and energy sources. The involvement of cytoplasmic enzymes in ibuprofen biodegradation was confirmed. Within the tested actinobacteria, Rhodococcus cerastii IEGM 1278 was capable of complete oxidation of 100 μg/L and 100 mg/L of ibuprofen in 30 h and 144 h, respectively, in the presence of an alternative carbon source (n-hexadecane). Besides, the presence of ibuprofen induced a transition of rhodococci from single- to multicellular lifeforms, a shift to more negative zeta potential values, and a decrease in the membrane permeability. The initial steps of ibuprofen biotransformation by R. cerastii IEGM 1278 involved the formation of hydroxylated and decarboxylated derivatives with higher phytotoxicity than the parent compound (ibuprofen). The data obtained indicate potential threats of this pharmaceutical pollutant and its metabolites to biota and natural ecosystems.

Analysis of the biodegradative and adaptive potential of the novel polychlorinated biphenyl degrader Rhodococcus sp. WAY2 revealed by its complete genome sequence

The complete genome sequence of Rhodococcus sp. WAY2 (WAY2) consists of a circular chromosome, three linear replicons and a small circular plasmid. The linear replicons contain typical actinobacterial invertron-type telomeres with the central CGTXCGC motif. Comparative phylogenetic analysis of the 16S rRNA gene along with phylogenomic analysis based on the genome-to-genome blast distance phylogeny (GBDP) algorithm and digital DNA–DNA hybridization (dDDH) with other Rhodococcus type strains resulted in a clear differentiation of WAY2, which is likely a new species. The genome of WAY2 contains five distinct clusters of bph, etb and nah genes, putatively involved in the degradation of several aromatic compounds. These clusters are distributed throughout the linear plasmids. The high sequence homology of the ring-hydroxylating subunits of these systems with other known enzymes has allowed us to model the range of aromatic substrates they could degrade. Further functional characterization revealed that WAY2 was able to grow with biphenyl, naphthalene and xylene as sole carbon and energy sources, and could oxidize multiple aromatic compounds, including ethylbenzene, phenanthrene, dibenzofuran and toluene. In addition, WAY2 was able to co-metabolize 23 polychlorinated biphenyl congeners, consistent with the five different ring-hydroxylating systems encoded by its genome. WAY2 could also use n-alkanes of various chain-lengths as a sole carbon source, probably due to the presence of alkB and ladA gene copies, which are only found in its chromosome. These results show that WAY2 has a potential to be used for the biodegradation of multiple organic compounds.

Features of diclofenac biodegradation by Rhodococcus ruber IEGM 346

This study investigated the ability of rhodococci to biodegrade diclofenac (DCF), one of the polycyclic non-steroidal anti-inflammatory drugs (NSAIDs) most frequently detected in the environment. Rhodococcus ruber strain IEGM 346 capable of complete DCF biodegradation (50 µg/L) over 6 days was selected. It is distinguished by the ability to degrade DCF at high (50 mg/L) concentrations unlike other known biodegraders. The DCF decomposition process was accelerated by adding glucose and due to short-term cell adaptation to 5 µg/L DCF. The most typical responses to DCF exposure observed were the changed ζ-potential of bacterial cells; increased cell hydrophobicity and total cell lipid content; multi-cellular conglomerates formed; and the changed surface-to-volume ratio. The obtained findings are considered as mechanisms of rhodococcal adaptation and hence their increased resistance to toxic effects of this pharmaceutical pollutant. The proposed pathways of bacterial DCF metabolisation were described. The data confirming the C-N bond cleavage and aromatic ring opening in the DCF structure were obtained.

Advanced Rhodococcus Biocatalysts for Environmental Biotechnologies

The review is devoted to biocatalysts based on actinobacteria of the genus Rhodococcus, which are promising for environmental biotechnologies. In the review, biotechnological advantages of Rhodococcus bacteria are evaluated, approaches used to develop robust and efficient biocatalysts are discussed, and their relevant applications are given. We focus on Rhodococcus cell immobilization in detail (methods of immobilization, criteria for strains and carriers, and optimization of process parameters) as the most efficient approach for stabilizing biocatalysts. It is shown that advanced Rhodococcus biocatalysts with improved working characteristics, enhanced stress tolerance, high catalytic activities, human and environment friendly, and commercially viable are developed, which are suitable for wastewater treatment, bioremediation, and biofuel production.

Biodegradation of emerging pollutants: focus on pharmaceuticals

A priority environmental problem is pollution and disturbance of natural environments by emerging pollutants ‒ substances of various origins and structures and with known and/or potential ecotoxic effects. One of the most dangerous groups of emerging pollutants is pharmaceutical substances due to their highly stable chemical structure and pronounced biological activity. They are found in soil, bottom sediments, surface, sewage, groundwater and drinking water. Uncontrolled release of pharmaceuticals in open ecosystems is potentially dangerous, entailing environmental consequences. Their negative impacts on living organisms are evident. This has driven the search for effective ways to neutralise persistent pollutants. In Russia, pharmaceutical pollution of the environment has commenced recently and is still presented as research with a local focus. In particular, the dynamics and metabolic mechanisms of pharma pollutants by Rhodococcus actinobacteria, outstanding among other microorganisms for their capacity to degrade a great diversity of degradable pollutants, are most intensively investigated. These studies are implemented at the junction of organic chemistry, molecular biology, biotechnology, and pharmacology. They include a set of interrelated fundamental tasks, such as developing drug detection methods in the cultivation media of microorganisms, elucidating the relationships between the systematic affiliation of microorganisms and their ability to degrade chemically different drug substances, as well as studying the degree of biodegradability and toxic effects of new compounds on the degrading microorganisms, and also the features of their decomposition and co-metabolism. Solving these tasks is important to enable understanding of the environmental fate of pharmaceuticals and to create prerequisites for innovative technical solutions in the advanced treatment of pharmaceutical wastewater. It is also essential for the development of environmentally safe approaches to hazardous pharmaceutical waste management.